MotIV (version 1.28.0)

motifMatch: Motifs Matches Analysis

Description

Search for motifs matches corresponding to PWM.

Usage

motifMatch(inputPWM, database=jaspar, DBscores=jaspar.scores, cc="PCC", align="SWU", top=5, go=1, ge=0.5)

Arguments

inputPWM

A list of PWM.

database

A list of PWM corresponding to the database.

DBscores

A matrix object containing the scores associated to the database.

cc

The metric name to be used

align

The Alignment method to be used.

top

The number of identified transcription factors per motif.

go

Gap open penality.

ge

Gap extension penality.

Value

motiv object.

Details

For a set of PWMs given by inputPWM, this function realizes alignments with each motif of the database and returns the top best motifs. If no database is provided, the function will use jaspar by loading data(jaspar2010). If no DBscores is given, jaspar.scores from data(jaspar2010_scores) will be used. The e-value is computed according the matric name cc and is corrected by the DBscores.

References

S Mahony, PE Auron, PV Benos, DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies, PLoS Computational Biology (2007) 3(3):e61

See Also

generateDBScores

Examples

#####Database and Scores#####
path <- system.file(package="MotIV")
jaspar <- readPWMfile(paste(path,"/extdata/jaspar2010.txt",sep=""))
jaspar.scores <- readDBScores(paste(path,"/extdata/jaspar2010_PCC_SWU.scores",sep=""))

#####Input#####
data(FOXA1_rGADEM)
motifs <- getPWM(gadem)
motifs.trimed <- lapply(motifs,trimPWMedge, threshold=1)

#####Analysis#####
foxa1.analysis.jaspar <- motifMatch(inputPWM=motifs,align="SWU",cc="PCC",database=jaspar,DBscores=jaspar.scores,top=5)
summary(foxa1.analysis.jaspar )